X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=af52edad5c3f42dd974ce358195f19d29c62317d;hb=b9e759d4f273ff99675c6c1fc7fd91d791948b93;hp=80ed4c1e993451834244c29f6bd9ea5560499841;hpb=4fa02869e039bb879849419737510b4b29ea5a4c;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 80ed4c1..af52eda 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -23,16 +23,19 @@ package jalview.project; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertFalse; import static org.testng.Assert.assertNotNull; +import static org.testng.Assert.assertNotSame; import static org.testng.Assert.assertNull; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; import java.awt.Color; +import java.awt.Rectangle; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import javax.swing.JInternalFrame; @@ -47,8 +50,13 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; +import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.ContactListI; +import jalview.datamodel.ContactMatrix; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLocus; import jalview.datamodel.HiddenSequences; @@ -68,8 +76,10 @@ import jalview.gui.AlignViewport; import jalview.gui.AlignmentPanel; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; +import jalview.gui.OverviewPanel; import jalview.gui.PCAPanel; import jalview.gui.PopupMenu; +import jalview.gui.Preferences; import jalview.gui.SliderPanel; import jalview.io.DataSourceType; import jalview.io.FileFormat; @@ -90,6 +100,7 @@ import jalview.util.MapList; import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase @@ -99,6 +110,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { + if (Desktop.instance != null) + Desktop.instance.closeAll_actionPerformed(null); JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } @@ -159,8 +172,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertNotNull( ColourSchemeProperty.getColourScheme(viewport, viewport.getAlignment(), - viewport.getGlobalColourScheme() - .getSchemeName()), + viewport.getGlobalColourScheme().getSchemeName()), "Recognise T-Coffee score from string"); af.saveAlignment(tfile, FileFormat.Jalview); @@ -233,8 +245,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase boolean diffseqcols = false, diffgseqcols = false; SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); - for (int p = 0, pSize = af.getViewport().getAlignment() - .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, + pSize = af.getViewport().getAlignment().getWidth(); p < pSize + && (!diffseqcols || !diffgseqcols); p++) { if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) @@ -253,8 +266,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(__rcs.isSeqAssociated(), "Group Annotation colourscheme wasn't sequence associated"); - for (int p = 0, pSize = af.getViewport().getAlignment() - .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, + pSize = af.getViewport().getAlignment().getWidth(); p < pSize + && (!diffseqcols || !diffgseqcols); p++) { if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null, @@ -449,9 +463,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.assertEquals(Desktop.getAlignFrames().length, Desktop.getAlignmentPanels( af.getViewport().getSequenceSetId()).length); - Assert.assertEquals( - Desktop.getAlignmentPanels( - af.getViewport().getSequenceSetId()).length, + Assert.assertEquals(Desktop + .getAlignmentPanels(af.getViewport().getSequenceSetId()).length, oldviews); } @@ -586,6 +599,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3")); assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1")); assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1")); + /* + * test for patch release versions + */ + assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.4")); + assertFalse( + Jalview2XML.isVersionStringLaterThan("2.12.2.0b1", "2.12.2.0")); + assertFalse( + Jalview2XML.isVersionStringLaterThan("2.12.2.3", "2.12.2.2")); + } /** @@ -804,6 +827,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase "Mismatch PDBEntry 'Type'"); Assert.assertNotNull(recov.getFile(), "Recovered PDBEntry should have a non-null file entry"); + Assert.assertEquals( + recov.getFile().toLowerCase(Locale.ENGLISH) + .lastIndexOf("pdb"), + recov.getFile().length() - 3, + "Recovered PDBEntry file should have PDB suffix"); } } @@ -815,6 +843,95 @@ public class Jalview2xmlTests extends Jalview2xmlBase * @throws IOException */ @Test(groups = { "Functional" }) + public void testStoreAndRecoverAnnotationRowElementColours() + throws IOException + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("SEQ\tMNQ", + DataSourceType.PASTE); + + AlignViewport av = af.getViewport(); + AlignmentI al = av.getAlignment(); + SequenceI fsq; + fsq = al.getSequenceAt(0); + Annotation annots[] = new Annotation[fsq.getLength()]; + AlignmentAnnotation ala = new AlignmentAnnotation("Colour", "Annots", + annots); + annots[0] = new Annotation(1.0f); + annots[1] = new Annotation(2.0f); + annots[2] = new Annotation(3.0f); + annots[0].colour = Color.RED; + annots[1].colour = Color.GREEN; + annots[2].colour = Color.BLUE; + ala.validateRangeAndDisplay(); + al.getSequenceAt(0).addAlignmentAnnotation(ala); + al.addAnnotation(ala); + /* + * and colour by annotation + */ + AnnotationColourGradient acg = new AnnotationColourGradient(ala, + af.alignPanel.av.getGlobalColourScheme(), 0); + acg.setSeqAssociated(true); + acg.setPredefinedColours(true); + af.changeColour(acg); + Color seqcol[] = new Color[3]; + for (int iStart = fsq.findIndex(fsq.getStart()), i = 0; i < 3; i++) + { + seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas + .getSequenceRenderer() + .getResidueColour(fsq, iStart + i, null); + } + /* + * save project, close windows, reload project, verify + */ + File tfile = File.createTempFile( + "testStoreAndRecoverAnnotRowElemColors", ".jvp"); + tfile.deleteOnExit(); + new Jalview2XML(false).saveState(tfile); + // Desktop.instance.closeAll_actionPerformed(null); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + Assert.assertNotNull(af, "Failed to reload project"); + /* + * verify alignment annotation has colors + */ + av = af.getViewport(); + + ColourSchemeI loadedCscheme = av.getGlobalColourScheme(); + Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient, + "Didn't apply Annotation colour gradient"); + acg = (AnnotationColourGradient) loadedCscheme; + assertTrue(acg.isSeqAssociated()); + assertTrue(acg.isPredefinedColours()); + + al = av.getAlignment(); + fsq = al.getSequenceAt(0); + ala = fsq.getAnnotation()[0]; + Assert.assertNotNull(ala, "No annotation row recovered"); + Assert.assertNotNull(ala.annotations); + for (int iStart = al.getSequenceAt(0) + .findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++) + { + Assert.assertTrue(ala.annotations[i].colour != null); + Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour)); + Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas + .getSequenceRenderer() + .getResidueColour(fsq, iStart + i, null); + Assert.assertTrue(seqcol[i].equals(newseqcol), + "Sequence shading is different"); + + } + + } + + /** + * Configure an alignment and a sub-group each with distinct colour schemes, + * Conservation and PID thresholds, and confirm these are restored from the + * saved project. + * + * @throws IOException + */ + @Test(groups = { "Functional" }) public void testStoreAndRecoverColourThresholds() throws IOException { Desktop.instance.closeAll_actionPerformed(null); @@ -1035,7 +1152,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertEquals(fr.getFeatureFilter("type2").toStableString(), "(Score LE 2.4) AND (Score GT 1.1)"); assertEquals(fr.getFeatureFilter("type3").toStableString(), - "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)"); + "(AF Contains X) OR (CSQ:PolyPhen NE 0)"); } private void addFeature(SequenceI seq, String featureType, int score) @@ -1205,7 +1322,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, DataSourceType.PASTE); assertNotNull(af, "Didn't read in the example file correctly."); - + AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0]; SequenceI pep = ap.getAlignment().getSequenceAt(0); SequenceI cds = ap.getAlignment().getSequenceAt(1); @@ -1237,7 +1354,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the state", e); } Desktop.instance.closeAll_actionPerformed(null); - + new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0]; @@ -1270,4 +1387,227 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(dbRef instanceof GeneLocus); assertEquals(dbRef, dbref3); } + + /** + * test store and recovery of Overview windows + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testStoreAndRecoverOverview() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + + Cache.setProperty("SHOW_OVERVIEW", "false"); + Cache.setProperty(Preferences.USE_LEGACY_GAP, "false"); + Cache.setColourProperty(Preferences.GAP_COLOUR, Color.green); + Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.yellow); + Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "true"); + + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + + /* + * open and resize / reposition overview + */ + af.overviewMenuItem_actionPerformed(null); + OverviewPanel ov1 = af.alignPanel.getOverviewPanel(); + assertNotNull(ov1); + ov1.setFrameBounds(20, 30, 200, 400); + assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa"); + assertTrue(ov1.isShowHiddenRegions()); + + /* + * open a New View and its Overview and reposition it + */ + af.newView_actionPerformed(null); + af.overviewMenuItem_actionPerformed(null); + OverviewPanel ov2 = af.alignPanel.getOverviewPanel(); + assertNotNull(ov2); + assertNotSame(ov1, ov2); + ov2.setFrameBounds(25, 35, 205, 405); + assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original"); + assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1"); + + File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + /* + * change preferences (should _not_ affect reloaded Overviews) + */ + Cache.setProperty("SHOW_OVERVIEW", "true"); + Cache.setProperty(Preferences.USE_LEGACY_GAP, "true"); + Cache.setColourProperty(Preferences.GAP_COLOUR, Color.blue); + Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.orange); + Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "false"); + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + + /* + * workaround: explicitly select View 1 (not in focus after restore) + */ + af.tabSelectionChanged(1); + + /* + * verify restored overview for View 1 + */ + ov2 = af.alignPanel.getOverviewPanel(); + assertEquals(ov2.getCanvas().getGapColour(), Color.green); + // 'non-legacy' colouring uses white for non-gapped residues + assertEquals(ov2.getCanvas().getResidueColour(), Color.white); + assertEquals(ov2.getCanvas().getHiddenColour(), Color.yellow); + assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1"); + assertEquals(ov2.getFrameBounds(), new Rectangle(25, 35, 205, 405)); + assertTrue(ov2.isShowHiddenRegions()); + + /* + * verify restored overview for Original view + */ + af.tabSelectionChanged(0); + ov1 = af.alignPanel.getOverviewPanel(); + assertEquals(ov1.getCanvas().getGapColour(), Color.green); + // 'non-legacy' colouring uses white for non-gapped residues + assertEquals(ov1.getCanvas().getResidueColour(), Color.white); + assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow); + assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original"); + assertEquals(ov1.getFrameBounds(), new Rectangle(20, 30, 200, 400)); + assertTrue(ov1.isShowHiddenRegions()); + } + + /** + * Test that a view with no Overview is restored with no Overview, even if + * 'Open Overview' is selected in Preferences + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testStoreAndRecoverNoOverview() throws Exception + { + Cache.setProperty("SHOW_OVERVIEW", "false"); + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE); + + File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + Cache.setProperty("SHOW_OVERVIEW", "true"); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + + assertNull(af.alignPanel.getOverviewPanel()); + } + + /** + * Test that a view from an older version of Jalview is restored with Overview + * automatically shown when the preference is set + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testAutoShowOverviewForLegacyProjects() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + Cache.setProperty("SHOW_OVERVIEW", "true"); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile.jvp", DataSourceType.FILE); + + Cache.setProperty("SHOW_OVERVIEW", "false"); + assertNotNull(af.alignPanel.getOverviewPanel()); + } + + /** + * Test that loading example.jvp, doing some stuff, then hitting reload + * doesn't leave the modified window still open + * + * See JAL-4127 - interactively performing the same actions and reloading + * works fine, but programmatically they do not + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = false) + public void testReloadActuallyReloads() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile.jvp", DataSourceType.FILE); + af.getViewport().getColumnSelection().addElement(3); + af.hideSelColumns_actionPerformed(null); + af.newView("new", true); + af.reload_actionPerformed(null); + Thread.sleep(30); + // af exists still but isn't shown + assertTrue(af.isClosed()); + } + + @Test(groups = { "Functional" }) + public void testPAEsaveRestore() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE); + AlignmentI al = af.getViewport().getAlignment(); + // PAE matrices are added as reference annotation to the dataset sequence + // at least for now. + SequenceI sq = al.getSequenceAt(0).getDatasetSequence(); + int i = sq.getLength(); + float[][] paevals = new float[i][i]; + for (i = i - 1; i >= 0; i--) + { + for (int j = 0; j <= i; j++) + { + paevals[i][j] = ((i - j < 2) + || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f; + paevals[j][i] = paevals[i][j]; + } + } + PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals); + String content = ContactMatrix.contactToFloatString(dummyMat); + Assert.assertTrue(content.contains("\t1.")); // at least one element must be + // 1 + float[][] vals = ContactMatrix.fromFloatStringToContacts(content, + sq.getLength(), sq.getLength()); + assertEquals(vals[3][4], paevals[3][4]); + dummyMat.makeGroups(0.5f, false); + Assert.assertNotSame(dummyMat.getNewick(), ""); + AlignmentAnnotation paeCm = sq.addContactList(dummyMat); + al.addAnnotation(paeCm); + File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix", + ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + AlignmentI newAl = af.getViewport().getAlignment(); + SequenceI newSeq = newAl.getSequenceAt(0).getDatasetSequence(); + // check annotation of the expected type exists + Assert.assertEquals(newSeq.getAnnotation().length, 1); + Assert.assertEquals(newSeq.getAnnotation()[0].graph, paeCm.graph); + + // check a contact matrix was recovered + Assert.assertEquals(newSeq.getContactMaps().size(), 1); + // and can be found for the annotation on the sequence + ContactMatrixI restoredMat = newSeq + .getContactMatrixFor(newSeq.getAnnotation()[0]); + Assert.assertNotNull(restoredMat); + for (i = sq.getLength() - 1; i >= 0; i--) + { + ContactListI oldCM = dummyMat.getContactList(i), + newCM = restoredMat.getContactList(i); + for (int j = oldCM.getContactHeight(); j >= 0; j--) + { + Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j)); + } + } + Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups()); + Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups()); + Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree()); + Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick()); + + } + }